Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_013683292.1 ARCVE_RS02945 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000194625.1:WP_013683292.1 Length = 328 Score = 408 bits (1048), Expect = e-118 Identities = 209/332 (62%), Positives = 254/332 (76%), Gaps = 4/332 (1%) Query: 1 MHKICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALD 60 M +I VI GDGIGKEV+ A + VLE LPFE+V+ EAGDE Y++ GKALP+ET+E Sbjct: 1 MKRITVIPGDGIGKEVMQAAMLVLEELNLPFEYVWMEAGDEAYEKYGKALPDETLEECKK 60 Query: 61 CDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEGLYK 120 DAVLFGAAGETAADVIV+LR L+T+ANIRP K+Y+GVKCL +D VIVRENTE LYK Sbjct: 61 SDAVLFGAAGETAADVIVRLRFELETFANIRPAKSYRGVKCLYDGVDIVIVRENTECLYK 120 Query: 121 GIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLTDGL 180 G+E E+ EG+T RVIT K ERI RFAF LAR + KVT HKANV+K T GL Sbjct: 121 GLEFEVAEGVTEGIRVITRKGSERIARFAFELARREGRK----KVTALHKANVMKKTCGL 176 Query: 181 FKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGL 240 F+ + +VA +Y DI+ DYYIDA MY++ P FDV+VT+N+FGDI+SD AAG VGGL Sbjct: 177 FRDVCREVARDYSDIEFNDYYIDAACMYLVMDPHRFDVIVTTNMFGDIVSDLAAGLVGGL 236 Query: 241 GLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKAL 300 G+APSANIG+ H +FEPVHGSAPDIAGK IANP+A IL+AV+MLR+ G + A +VEKAL Sbjct: 237 GMAPSANIGERHAIFEPVHGSAPDIAGKGIANPSAMILTAVMMLRHFGYLDEAARVEKAL 296 Query: 301 EEVLALGLTTPDLGGNLNTFEMAEEVAKRVRE 332 EEV+ G TTPDLGGNL T EMA+EV +++E Sbjct: 297 EEVIVEGRTTPDLGGNLKTMEMAQEVVNKLKE 328 Lambda K H 0.318 0.138 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 390 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 328 Length adjustment: 28 Effective length of query: 305 Effective length of database: 300 Effective search space: 91500 Effective search space used: 91500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory